|
| Status |
Public on Oct 16, 2019 |
| Title |
S1-3D TB |
| Sample type |
RNA |
| |
|
| Source name |
S1 cells embedded and grown in 3D rBM and treated with TRAIL
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: breast epithelium
|
| Treatment protocol |
Cells were pre-treated with caspase inhibitors DEVD-CHO and Ac-IETD-CHO (1μM, respectively) at least 2 hours before TRAIL treatment (1 ug/ml) for 8hrs.
|
| Growth protocol |
HMT-3522 S1 cells were propagated as monolayers on rBM-coated tissue culture plastics in chemically defined medium comprising of DMEM/F12, prolactin (0.15 IU/ml), insulin (250 ng/ml), hydrocortisone (1.4 μM), sodium selenite (2.6 ng/ml), β-Estradiol (0.1 nM), Apo-transferrin (10 μg/ml), and EGF (10 ng/ml). For 3D culture, S1 cells were embedded in 3D rBM (Matrigel, BD Bioscience) and grown for 12 days to form 3D acini organoids before the subsequent treatment.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
TRIzol extraction of total RNA was performed according to the manufacturer's instructions. The resulted RNA samples were further purified by Rneasy Mini Kit (Qiagen).
|
| Label |
biotin
|
| Label protocol |
Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
|
| |
|
| Hybridization protocol |
Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Drosophila Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
|
| Scan protocol |
Arrays were scanned by a confocal scanner.
|
| Description |
S1 cells were embedded in 3D rBM and treated with TRAIL (1ug/ml) for 8 hours, replication 2.
|
| Data processing |
Affymetrix .cel files were processed with ArrayAssist Lite (v3.4, Stratagene). The files were imported and processed with the GC-RMA algorithm to yield probe set intensities and additionally, Affymetrix Preset, Absent, Marginal flags were computed. These values were exported in .chp files, which were subsequently imported into the Partek Genomics Suite software (v6.2).
|
| |
|
| Submission date |
Oct 15, 2019 |
| Last update date |
Oct 16, 2019 |
| Contact name |
Kelvin Kun-Chih Tsai |
| Organization name |
Taipei Medical University
|
| Department |
Graduate Institute of Clinical Medicine, College of Medicine
|
| Lab |
Laboratory of Advanced Molecular Therapeutics
|
| Street address |
7F, 250 Wuxing St, Xinyi Dist
|
| City |
Taipei City |
| ZIP/Postal code |
11031 |
| Country |
Taiwan |
| |
|
| Platform ID |
GPL96 |
| Series (1) |
| GSE138900 |
Gene expression profile of HMT3522 S1 cells grown on 2D and in 3D matrix in response to the death ligand TRAIL |
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